Sample polynucleotides may be subjected to electrophoresis in the presence of reference polynucleotides having a known size. Sample polynucleotides and reference polynucleotides having the same size generally exhibit the same mobility when subjected to electrophoresis. The size of the sample polynucleotides may be determined using migration times of the sample polynucleotides and of the reference polynucleotides.
Detection methods, such as fluorescence resulting from intercalating dyes, are typically sensitive to the presence of both the sample polynucleotides and the reference polynucleotides. Thus, electrophoresis data from a separation of sample polynucleotides and reference polynucleotides may include a sample polynucleotide peak that is obscured by a peak resulting from one of the reference polynucleotides.